Simulation study on “ torsion ” and local structure of chromosome: Loop structure via torsion-adding loop extrusion

Abstract

The bending and twisting deformations of biopolymers have attracted considerable interests. In this paper, we propose a ladder-type polymer chain minimal model which describes DNA-like polymers’ bending and twisting elasticities within the framework of coarse-grained molecular dynamics simulation. Applying the model for a loop extrusion process, which introduces loop and twist on the chain, we obtained the stable twisted loop structures and observed the conversion between bend-elastic and twist-elastic energies. Moreover, we computed the linking number, a topological invariant for wound and twisted structures with fixed ends, and confirmed that the energy conversion proceeds under conservation of the linking number.